[Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch)

Dan Bolser dan.bolser at gmail.com
Thu Jul 8 10:33:19 EDT 2010


The bugtracker seems broken (or taking a painfully long time to log me
in). So here is my bug report before I forget:



Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace

Body:
The code had inconsistent use of the '_qualify' function, and one
instance of a hard-coded table name. These issues were not apparent
until "-namespace anything" was used.

First I got the fatal error:

DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist
at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
line 428, <GEN0> line 2.


which was due to a hard-coded table name. Then, after fixing, I got the error:

Loading bulk data into database...DBD::mysql::db do failed: Table
'dbolser.sheng_kai_sheng_kai_name' doesn't exist at
/homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
line 570, <GEN0> line 10000.


i.e. the prefix was being added to the table name twice.


I went through the code and tried to make all references to table
names consistent to ensure that bugs like this won't creep in again...
however, the code for this module isn't very consistent.

(See patch attached).
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